


Hidden Truths

by blackrose_17



Series: Hidden Paths [1]
Category: The Avengers (Marvel Movies), The Avengers (Marvel) - All Media Types, Torchwood
Genre: Alternate Universe - Canon Divergence, Community: hc_bingo, Hurt Ianto Jones, Hurt/Comfort, M/M, Mind Control, What-If
Language: English
Status: Completed
Published: 2014-04-13
Updated: 2014-04-13
Packaged: 2018-01-19 04:58:54
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings, No Archive Warnings Apply
Chapters: 1
Words: 3,783
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/1456354
Author URL: https://archiveofourown.org/users/blackrose_17/pseuds/blackrose_17
Summary: <blockquote class="userstuff">
              <p>To Torchwood Three Ianto Jones was the invisible one before and after Lisa but they learn that not all is what it seems to be as they learn the truth about Ianto Jones and it forever changes what they thought they knew as fact.</p>
            </blockquote>





	Hidden Truths

**Author's Note:**

> As usual I do not own Torchwood or the Avengers. This was written for the April challenge for the h_c bingo and is currently unbeta, so please excuse any mistakes but I wanted this up as I am working on a borrowed laptop until mine is fixed. This is a what-if Ianto's actions weren't his own, there is more than likely going to be a sequel in the future expanding on Ianto's healing.

Ianto Jones was the outcast of Torchwood Three, he was the unwanted member of the team and that was before the others learned of Lisa hidden in the basement, know he was the pariah, the forgotten until coffee was needed or something cleaned. Since his return weeks ago Ianto moved about the Hub even more of a ghost than before, slowly fading away from his guilt and pain he had caused the others, aching for forgiveness that would never be given, he was wearing himself out trying to make amends and to start earning their trust once again, they noticed but their rage and anger at the youngest member was still too great to overcome their growing worries for the pale man, they were just to raw to notice that they were losing Ianto, until it was too late.

To Jack and Tosh’s shame it was late into the day when someone finally noticed that Ianto was nowhere to be seen and that was only because the lack of caffeine had finally hit them.

“Oi, Harkness where have you gotten that bloody traitor hidden? I need so coffee and since that’s his job telling him to get on it.” Owen demanded his voice harsh and cold, he was a long way from forgiving Ianto.

Coming out of his office Jack wore a frown; he couldn’t remember seeing Ianto all day, not that he had really been paying attention, he might have allowed Ianto back but he was a long way from forgiving the man and wanted little to do with him. “I haven’t seen him all day, have you checked the Archives?” That was where Ianto had taken to hiding out for the day or the tourist office, anywhere that was far enough away from the coldness that engulfed the Hub whenever Ianto entered the room.

While Jack was talking Tosh pulled up the Hub CCTV scanning for any sight of Ianto, when that didn’t show anything Tosh they did a heat scan after adjusting for their non-human guest only four heat signatures registered and Tosh felt a sense of worry and dread filling her as she pulled up the footage from last night, what she saw broke her heart. Despite the footage being without colour or sound it was clear to Tosh that Ianto was sick, she watched as the young Welshman body doubled over and clutch his head as he stumbled against the wall, holding onto it for support. “What have we done?” Tosh had vowed that after everything that had happen she would take the time to truly notice Ianto but that hadn’t happened, she allowed the others feelings of rage and betrayal keep her from offering an branch of friendship to Ianto, she hadn’t wanted Owen to hate her and now she hated herself and them just a little bit.

Owen scowled and crossed his arms over his chest. “It’s not my job to keep an eye on Jones, if you recall I didn’t even want that bloody bastard back in the Hub not after what he had done.”

Seated at her desk Gwen nodded her head in agreement with Owen, both of them had approached Jack and spoke their minds, stating that they couldn’t trust Ianto and wanted him nowhere near them. Gwen personally thought that they should have just Retconned Ianto and washed their hands of him, after all he had nearly got her converted and she knew she would never be able to trust Ianto again. “Maybe Ianto decided he had enough and Retconned himself.” Gwen piped up.

Jack went cold at that, he had figured if Ianto was going to do anything it would have been on his suspension but given that he hadn’t spoke to the man in the two weeks he had been back, unless it was giving an order, he was still to hurt to truly address Ianto or to make sure the others took it easy on him.

“Did any of you notice that Ianto was sick? Because I didn’t.” Tosh’s quite voice broke the tense silence and all eyes flew to her. Unshed tears shone in her eyes but despite them she glared at each of them. “We treated Ianto like he was nothing, like he was lower than dirt because he worked at Torchwood One, not one of us took the time to truly get to know him and look what happened! He didn’t come to us about Lisa, because we gave him no reason to trust us. Now we treat him like he is a disease! That the only thing he truly is worthy of is cleaning up our shit! He’s sick and not one of us noticed or took the time to care. Well not anymore, I care about Ianto and I’m not going to let what the rest of you think influence me anymore.” With that said Tosh snatched her jacket from the back of her chair and her pursed and stalked out the door, leaving the other three members of Torchwood staring after her in stun silence.

Jack knew Tosh was right; they had never given Ianto any reason to trust them, to trust him. _‘Face it Jack you saw a pretty face and wanted Ianto around to seduce but then something new and shiny came along and you forgot all about Ianto. Why was it that I would take the time to make Gwen apart of the team but not Ianto? Was it because he was a member of Torchwood One? Rose would have been ashamed of my treatment of Ianto, she would have smacked me upside the head if she saw how I treated Ianto.’_ Jack knows that both Rose and the Doctor would have been so disappointed in him and not just his treatment towards Ianto but to the other survivors of Torchwood One, Jack had washed his hands of him and he had no clue what happened to any of them. _‘You really are a bastard Jack Harkness. Ianto did what he did for love and I can’t say the same.’_

It wouldn’t be easy but it was time from him to change, to become the man that both Rose and the Doctor saw in him. “Owen, get your kit, we have a sick teammate to check on!” Jack ordered.

“What? You want me to help that man, after what he did?” Owen demanded.

Jack levelled a dark glare at Owen. “Ianto did what he did for love; you can’t tell me you wouldn’t have done the same thing?” He asked already knowing the answer. “Because I know I would have.” Jack ran a hand through his hair; he knew that if it had been Rose partly converted he would have done everything in his power to save her.

Owen paled; he knew deep in his heart that if that had been Katie he would have done the same thing, hell he would have happily ripped apart the whole world if it meant saving her. “Damn it.” Owen grumbled under his breath as he turned and headed towards the medical bay.

Knowing that she had missed something Gwen blinked at Owen’s change of heart. “Jack, is Ianto really any of our concern? Wouldn’t it be better just to let him go? Surely this isn’t the place for him, we can’t trust him and how can we work with someone we don’t trust?” Gwen asked.

Jack could hardly believe what he was hearing from Gwen, the woman he brought in to remind them all what it was like to be human again. “Gwen, can you honestly tell me that if it had been Rhys you wouldn’t have done the same thing? If you lost Rhys you wouldn’t do everything in your power to save him? I brought you because of your compassion; shouldn’t you be showing that compassion to our teammate who watched his world fall apart for the second time in his young life?” Jack asked. “If you can muster up some concern then you are welcomed to come with us to check on Ianto but if you can’t, then you can monitor things and alert us if anything comes up.” Jack informed her as he turned on his heel and stalked off leaving a shocked Gwen staring at his back.

******

The feeling of dread that had been building in Tosh’s stomach since she left the Hub had only grown as she reached Ianto’s flat, working for her own secret organization she easily recognized the unmarked black SUV’s that surrounded Ianto’s flat. Fear griped her that UNIT had somehow found out about Lisa and had come for Ianto. Tosh flew out of her car and she honestly couldn’t remember anything until she was standing in front of Ianto’s door, her hand on the doorknob and with a twist opened.

It wasn’t UNIT that was standing in the middle of Ianto’s bare flat, a fact that took Tosh back for a moment but a slightly older man, dressed in a suit similar to Ianto’s and with an easy going smile on his face. “You must be Toshiko Sato; it’s nice to meet you. I’m Agent Phil Coulson of SHIELD.”

Tosh blinked, she knew of SHIELD, everyone knew of SHIELD, they were the ones you didn’t want as an enemy, yet worry about her teammate overruled any fear Tosh might have had. “Where’s Ianto?” She demanded to know.

The smile faded from Phil’s face as if he was pleased with her question. “Agent Ianto Jones is no longer your concern.” Phil informed her as gently as he could.

“That’s where you are wrong, Ianto is ours and I would like to know what SHIELD has done with my agent.” Jack’s cool voice came from behind Tosh.

Tosh felt her body relax as Jack came up behind her and she was surprised to see both Owen and Gwen with him.

“If you treat all your agents the way you treated Ianto, I’m surprised you have a team at all.” It wasn’t Coulson who spoke but the beautiful redhead woman who emerged from the kitchen, a deadly look in her eyes.

Completely ignoring and dismissing the group before him Phil focused all his attention on Natasha. “How is Agent Jones?” He asked, unable to fully keep the worry fully from his voice.

Natasha’s eyes soften just the slightest and a teasing smile graced her lips, “You’re boytoy says you were right, there was something cyber planted in the base of Ianto’s skull,” All teasing left Natasha at this point, “what Tony can determine it seemed to have been sending signals to his brain, controlling him. Clint says that the doctors have determined that it is Cybermen technology.”

Ignoring the comment about Stark being his boytoy Phil nodded his head, what he and Tony got up to was no one’s business but his and Tony’s. “That makes sense I figured something was off when the reports claimed that Ianto said Lisa Hallet was his girlfriend, I think Agent Barton would have objected to that claim. We should have pulled him out sooner, instead of letting him stay undercover.”

Natasha shook her head. “That wouldn’t have worked; we all know how stubborn Ianto can be when he’s put his mind to something. Director Fury made it clear he wanted a full report on Torchwood One and Three to see how stable they are.” Natasha shot a dark look at the gaping members of Torchwood. “And from what I can see they are not very stable at all.”

The four members of Torchwood bristled at her words but it was Gwen who spoke without thinking, a fact that Jack was beginning to see would never change in his newest member and would lead her into trouble one of these times. “Excuse me, but who in the hell do you think you are to judge us? Ianto Jones is a traitor who brought a known danger into our base, a danger that nearly had me converted! And now you want us to believe some story about how Ianto was being controlled? Please, what kind of fools do you take us for?”

Natasha was not a woman you wanted as your enemy but there was something about Gwen Cooper that just rubbed her the wrong way. “I am the woman known as the Black Widow; I have seen and done things that would make your stomach curl. But I take care of those who are mine, unlike you.” Natasha growled.

Despite the fear snaking up her spine Gwen held her head high. “And just what is that suppose to mean?”

Natasha raised an eyebrow. “According to all reports you are the so-called ‘heart of Torchwood’ meant to remind them all what it means to be human. Yet from what we have seen you care nothing about your teammates, both past and present, all you care about is what you want. Does your poor suffering boyfriend know how you lust after two of your male teammates or your past affairs? If you were truly the heart or the carer you claim to be, you would have tried to reach out to Ianto before and after the events that had happen, instead you wanted to Retcon him and wash your hands of him. Not very caring from where I’m standing.”

“You hacked my systems, didn’t you?” Tosh demanded, her systems were supposed to be unhackable.

Phil sent her a soft smile. “If it makes you feel better it took Tony Stark almost five hours to hack them, he was rather impressed.”

Tosh stared open mouth at Phil. “Tony Stark? Thee Tony Stark was impressed with me?” She could hardly believe it and she knows she shouldn’t feel like a giddy schoolgirl, but come on; Tony Stark had been impressed with her.

Despite his rage at his base being hacked into Jack couldn’t help but feel happy for Tosh, it was rare for Tosh to be acknowledge for her talents. “Back to the matter at hand, what have you done with my Agent?” Jack demanded.

Phil raised an eyebrow, unimpressed with Jack’s demands or the dark look he sent his way. “Agent Ianto Jones was never a member of Torchwood One, he had been placed there with a few others to investigate them, and SHIELD had been a worried about Yvonne Hartman’s desire to return to the golden age. Ianto Jones was the only agent to make it out alive; the others were lost in the fall of Torchwood One. Despite the advice of our doctors Ianto agreed to go undercover and observe the reneged and wildcard known as Torchwood Three. If we had known what we now know we would have never let him go. Ianto Jones was never involved with Lisa Hallet, in fact to our knowledge he’s never even met her before she was converted.” Phil informed them.

“Bullshit!” Owen snarled. “He brought that thing into our base because he was desperate to save her and we are supposed to believe that she was a stranger after he nearly destroyed us all?”

Phil looked unimpressed with Owen’s outburst. “Believe what you wish Dr Harper, but I have known Ianto all of his life and I know for a fact that he has been involved with Agent Barton for almost four years. Ianto would not cheat or string along anyone, if had met someone he would have done the honourable thing and ended his relationship with his fellow agent. We already knew something was wrong before we received word from Ianto that something was wrong. We arrived late last night to find him barely conscious, clutching his head as he whimpered in pain. Lucky for us Stark had made a pest of himself and tagged along and one of his scans revealed something that didn’t belong.”

Jack figured where this was gone and felt sick to his stomach. “Cyber control.”

Natasha nodded her head. “Correct, we believe that it had been implanted some time during the battle at Torchwood One and the Cyberwoman that had once been Lisa used it to save herself, convincing Ianto that she was the most important thing in his life and he needed to save her.” She could see the growing devastation on their faces but couldn’t find it in her to care, they had hurt someone she cared about and in her mind they deserved every bit of pain they were feeling. “You would have known this if any of you truly bother to take the time to get to know Ianto, instead of abusing his kind heart.”

Jack winced at Natasha’s jab but knew she only spoke the truth and he reached out to pull Tosh into his arms, knowing that she was going to be the one to take this the hardest.

Owen couldn’t believe that he had missed it, and he had no excuse he had never taken the time to really look after Ianto, he had never hid his dislike of the young man or where he came from and that had only got worse when he learned about Lisa, he didn’t want to see him, he wanted to be justified in his hatred of the young man. And in his ignorance he had missed the piece of cyber technology using Ianto and they would have condemned an innocent man to losing his memory or worse if Jack hadn’t decided against protocol. Owen felt like he was going to be sick as a wave of nausea rose up in him as he realised how he treated a man who had been a prisoner in his own mind.

A gasp escaped Gwen’s lips as what the two SHIELD agents were telling them finally hit home. “Oh my god, what have we done? You have to give Ianto back to us so we can make this right.” She demanded, not because she truly cared about Ianto but more to ease her own conscious.

Ice poured off of Natasha in waves as she told them in chipped voice, “Ianto will never be returning to Torchwood Three, after the surgery to remove the cyber plant, he will need counselling not only to deal with survivor’s guilt but also to come to terms with what he had done under the Cyberman’s control. Why would he return to a place where no one cared about him, unless it was to serve their every need?”

Jack, Owen and Tosh could hear the unsaid _‘Just like he had the Cyberman?’_ They knew that Ianto Jones would never return to them and they would have to live with that guilt and knowledge of how they failed Ianto Jones.

Jack lifted his head to met Phil’s eyes. “Take care of him, like we couldn’t.”

Phil could easily read the sorrow in both Jack and Toshiko’s eyes and the guilt in Owen’s and knew that they would live with the knowledge of how they failed and isolated the youngest member of their team. “I will and don’t give up hope, I know my son well and he will forgive you all he will need is time. And if you really wanted to make things right with Ianto, look into the other survivors; show them that they are not alone and that you care. They should not be judged or blamed for the actions of the few; most of them had no clue what Yvonne was up to.” Phil advised them.

Once he was over the surprise that the man before them was Ianto’s father, Jack could see Phil’s point, for so long he had let his hatred of Yvonne and the fact that he had lost Rose cloud his responsibilities to those left behind, he was a leader and it had been his job to look after those who survived. “I will. I’ll ensure that they get the help they need and deserve.”

******

High in the air, onboard the private plane of Tony Stark, Clint Barton was grateful to be leaving Cardiff far behind them as he focused all his attention on his lover who lay curled up next to him, heavily sedated to ensure he had the most comfortable ride home. Looking at Ianto’s pale face Clint was grateful that Tony had insisted that they take his private plane, it offered a much more comfortable ride back to New York.

“C’int?” Ianto’s slurred voice broke the silent plane.

Clint smiled down at Ianto. “Hey, you should be resting.”

Ianto blinked his heavy eyelids and smiled goofy at his partner. “We going home?” He forced out despite the call of the drugs.

Unable to resist Clint leaned down and brushed a gentle kiss on Ianto’s forehead. “Yeah, we’re going home and I’m not letting you out of my sight again.”

“Okay.” Ianto let a smile grace his lips before letting the drugs drag him back under.

Tony had enough sense to keep quiet during the moment between the two lovers, knowing that he would have plenty of blackmail by the time they landed it wasn’t every day that he got to watch the cool and cocky agent acting all loving. _‘Plus I do have a certain agent in debt to me for borrowing my plane and Phil wanted me to stay back.’_ Oh yeah Tony had detail plans on how one Agent Coulson could pay him back for the use of his plane.

Watching Clint and Ianto, Tony knew that things were going to change, he knew the long road Ianto was going to have before him, having gone through it himself and he could say that it was never easy to live with the guilt of surviving or living with the knowledge of the damage you’ve done and will Ianto’s actions were not of his own it was it would still be a long road ahead of him. Even though Tony didn’t know Ianto he wanted to and not just because he was the son of Phil but because he seemed like someone amazing. _‘It’s going to be a tough road ahead of you kid, but you’ll have those who love and care about you to help you along the way and your biggest support is right next to you.’_ Pulling out his tablet Tony studied the cyber tech that JARVIS had found in Ianto’s head, he needed to know everything he could if he was going to help remove it safely from Ianto and give the young man his life back, still he couldn’t help but take one last look at Ianto who was curled up in Clint’s arms with the other man on guard to protect him from all dangers and hoped he could someday have that with Phil.


End file.
